{'WT': '../test/Moazzen/WT_E11_5/sample_filtered_feature_bc_matrix', 'KO': '../test/Moazzen/Mut_E11_5/sample_filtered_feature_bc_matrix'}
{'WT': '../test/Moazzen/WT_E11_5/sample_filtered_feature_bc_matrix', 'KO': '../test/Moazzen/Mut_E11_5/sample_filtered_feature_bc_matrix'}

Quality Plots

Basic QC plots & metrics

No description has been provided for this image

Table of basic QC metrics

n_genes_by_counts total_counts pct_counts_mt pct_counts_ribo doublet_score S_score G2M_score sample
mean median mean median mean median mean median mean median mean median mean median size
sample
KO 3193.389 2561.0 14489.261 5980.0 3.160 1.877 0.0 0.0 0.049 0.037 -0.005 -0.149 -0.005 -0.149 8365
WT 3272.712 2674.0 15085.768 6799.0 2.417 1.591 0.0 0.0 0.045 0.029 0.003 -0.148 0.003 -0.148 11229

Histograms

No description has been provided for this image

Filtering Thresholds

Min Max
n_genes_by_counts 155.0 10186.347402
total_counts 1059.0 35071.109421

Number of outliers based on provided criteria

Outlier MT-Outlier
sample
False WT 8429 10040
KO 7051 7010
True WT 2800 1189
KO 1314 1355

Remaining Cells after filtering based on outlier function

n_genes_by_counts total_counts pct_counts_mt pct_counts_ribo doublet_score S_score G2M_score sample
mean median mean median mean median mean median mean median mean median mean median size
sample
KO 3418.461 2866.0 12968.836 5597.0 2.128 1.813 0.0 0.0 0.049 0.039 -0.015 -0.157 -0.015 -0.157 5739
WT 3792.106 3361.0 13962.100 6637.0 2.248 1.979 0.0 0.0 0.049 0.034 0.033 -0.099 0.033 -0.099 7248

Scatter plots of confounders

No description has been provided for this image

DecontX contamination

No description has been provided for this image

Clustering prior to cell filtering

No description has been provided for this image

Regression of Variables

sample n_genes_by_counts log1p_n_genes_by_counts total_counts log1p_total_counts pct_counts_in_top_20_genes total_counts_mt log1p_total_counts_mt pct_counts_mt total_counts_ribo ... decontX_contamination decontX_clusters n_genes doublet_score predicted_doublet n_counts S_score G2M_score phase groups
AAACAAGCAATGAGCCAACGGGAA-1 WT 2957 7.992269 5382.0 8.591002 8.286882 76.0 4.343805 1.412115 0.0 ... 0.013997 1 2957 0.033079 False 5382.0 0.708197 0.708197 S 0
AAACAAGCACAGCAACAACGGGAA-1 WT 843 6.738152 2423.0 7.793174 27.445316 10.0 2.397895 0.412712 0.0 ... 0.044109 3 843 0.023555 False 2423.0 -0.412892 -0.412892 G1 1
AAACAAGCAGAGGCTTAACGGGAA-1 WT 2261 7.724005 3429.0 8.140316 6.824147 32.0 3.496508 0.933217 0.0 ... 0.031528 1 2261 0.018878 False 3429.0 -0.356001 -0.356001 G1 0
AAACAAGCATCGATAGACTTTAGG-1 WT 5243 8.564840 12701.0 9.449514 3.999685 41.0 3.737670 0.322809 0.0 ... 0.026544 2 5243 0.014218 False 12701.0 0.733244 0.733244 S 3
AAACAAGCATTGCCCAACTTTAGG-1 WT 3307 8.104099 6492.0 8.778480 10.921134 96.0 4.574711 1.478743 0.0 ... 0.037526 1 3307 0.043515 False 6492.0 0.123662 0.123662 S 0
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
TTTGTGAGTAGGTGACATGTTGAC-1 KO 5887 8.680672 16686.0 9.722385 7.473331 459.0 6.131227 2.750809 0.0 ... 0.069692 2 5887 0.235832 False 16686.0 0.195697 0.195697 S 4
TTTGTGAGTCCACAATATGTTGAC-1 KO 6926 8.843182 26409.0 10.181498 6.232724 439.0 6.086775 1.662312 0.0 ... 0.051976 1 6925 0.041409 False 26409.0 -0.138252 -0.138252 G1 8
TTTGTGAGTGAACGGTATGTTGAC-1 KO 4322 8.371705 11396.0 9.341105 12.267462 275.0 5.620401 2.413127 0.0 ... 0.154473 1 4322 0.084693 False 11396.0 -0.109296 -0.109296 G1 9
TTTGTGAGTGCTGATTATGTTGAC-1 KO 3852 8.256607 8126.0 9.002947 8.983510 81.0 4.406719 0.996800 0.0 ... 0.402884 2 3852 0.169399 False 8126.0 -0.218594 -0.218594 G1 7
TTTGTGAGTTACCGTGAGTAGGCT-1 KO 1393 7.239933 2029.0 7.615791 8.378512 25.0 3.258096 1.232134 0.0 ... 0.155729 1 1393 0.037975 False 2029.0 -0.329304 -0.329304 G1 2

12987 rows × 27 columns

Ambient RNA

<Axes: xlabel='decontX_clusters', ylabel='decontX_contamination'>
No description has been provided for this image

Session Information

Click to view session information 
-----
anndata             0.10.7
matplotlib          3.8.4
numpy               1.26.4
pandas              2.2.2
patchworklib        0.6.3
requests            2.32.3
scanpy              1.10.1
scipy               1.13.1
seaborn             0.13.2
session_info        1.0.0
tomlkit             0.12.5
-----
Click to view modules imported as dependencies 
PIL                         10.3.0
anyio                       NA
argcomplete                 NA
arrow                       1.3.0
asttokens                   NA
attr                        23.2.0
attrs                       23.2.0
babel                       2.14.0
bleach                      6.1.0
brotli                      1.1.0
bs4                         4.12.3
cerberus                    1.3.5
certifi                     2024.02.02
cffi                        1.16.0
charset_normalizer          3.3.2
colorama                    0.4.6
comm                        0.2.2
cycler                      0.12.1
cython_runtime              NA
dateutil                    2.9.0
debugpy                     1.8.1
decorator                   5.1.1
defusedxml                  0.7.1
dill                        0.3.8
executing                   2.0.1
fastjsonschema              NA
fqdn                        NA
h5py                        3.11.0
idna                        3.7
igraph                      0.11.5
ipykernel                   6.29.3
isoduration                 NA
jedi                        0.19.1
jinja2                      3.1.4
joblib                      1.4.2
json5                       0.9.25
jsonpointer                 2.4
jsonschema                  4.22.0
jsonschema_specifications   NA
jupyter_events              0.10.0
jupyter_server              2.14.1
jupyterlab_pygments         0.3.0
jupyterlab_server           2.27.2
kiwisolver                  1.4.5
lazy_loader                 0.4
legacy_api_wrap             NA
leidenalg                   0.10.2
llvmlite                    0.42.0
markupsafe                  2.1.5
matplotlib_inline           0.1.7
mistune                     3.0.2
mizani                      0.11.4
mpl_toolkits                NA
natsort                     8.4.0
nbclient                    0.10.0
nbconvert                   7.16.4
nbformat                    5.10.4
numba                       0.59.1
overrides                   NA
packaging                   24.0
pandocfilters               NA
parso                       0.8.4
patsy                       0.5.6
pickleshare                 0.7.5
pkg_resources               NA
platformdirs                4.2.2
plotnine                    0.13.6
pretty_jupyter              NA
prometheus_client           NA
prompt_toolkit              3.0.42
psutil                      5.9.8
pure_eval                   0.2.2
pycparser                   2.22
pydev_ipython               NA
pydevconsole                NA
pydevd                      2.9.5
pydevd_file_utils           NA
pydevd_plugins              NA
pydevd_tracing              NA
pygments                    2.18.0
pynndescent                 0.5.12
pyparsing                   3.1.2
pythonjsonlogger            NA
pytz                        2024.1
referencing                 NA
rfc3339_validator           0.1.4
rfc3986_validator           0.1.1
rpds                        NA
send2trash                  NA
setuptools                  70.0.0
six                         1.16.0
skimage                     0.22.0
sklearn                     1.5.0
sniffio                     1.3.1
socks                       1.7.1
soupsieve                   2.5
stack_data                  0.6.2
statsmodels                 0.14.2
texttable                   1.7.0
threadpoolctl               3.5.0
tinycss2                    1.3.0
tornado                     6.4
tqdm                        4.66.4
traitlets                   5.14.3
typing_extensions           NA
umap                        0.5.5
uri_template                NA
urllib3                     2.2.1
wcwidth                     0.2.13
webcolors                   1.13
webencodings                0.5.1
websocket                   1.8.0
yaml                        6.0.1
zmq                         26.0.3

-----
IPython             8.25.0
jupyter_client      8.6.2
jupyter_core        5.7.2
jupyterlab          4.2.1
-----
Python 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:36:13) [GCC 12.3.0]
Linux-6.8.0-35-generic-x86_64-with-glibc2.39
-----
Session information updated at 2024-06-07 11:33